Contents

Sometime before 2151, Archer killed his father in order to steal his designs for the warp five engine. In 2151, a Klingon warrior crash landed on Earth and, after being tortured and giving up information about the Klingon Empire and its location, prompted Starfleet to finish its designs for more powerful warships. Faced with the prospect of a larger empire with superior technology, Archer pursuaded the Emperor to fund the completion of the warp five engine, which Archer passed off as his own, and then volunteered his new warship for duty in learning about and suppressing the Klingons. (Deciphermodule: Through a Glass, Darkly)

The RPG "Through a Glass, Darkly" describes Archer as being a recently-promoted captain, who was then put in command of the Enterprise.

Archer was in line to become captain of the Enterprise himself, but AdmiralMaximilian Forrest deliberately gave up his rank for a captain's position and took command of the Enterprise instead. Archer openly protested, but was reduced to Commander and first officer of the Enterprise. Archer would later insist that this radical change in command was the result of a growing number of admirals at Starfleet Command plotting against him.

Archer maintained his post on the ship, hiding a deep hatred and jealousy for Forrest. This was furthered when Hoshi Sato, his lover during the time he believed he would command the Enterprise, left him to be with Forrest because of his new status. Archer never got over it. Forrest still kept Archer around as his right-hand, because he thought Archer "never lusted for power and glory". He was wrong, however. Archer had deep ambitions for his own command, which lay buried just beneath the surface. (ENTepisode: "In a Mirror, Darkly")

Archer engaged in criminal activities, such as bribery and espionage, gain intel for the Empire's benefit to wage the floundering war on the Anti-Imperial Rebellion. One such contact Archer had was a forced-labor worker in the employ of the Tholian Assembly. Before his contact was exposed and killed, he was able to transmit detailed scans of a ship in a Tholian drydock, the USS Defiant, and gave him the warp signature of a Tholian pilot who knew where the ship was.

Archer desperately tried to convince Forrest to mount a salvage operation, as the ship's technology could save the dying Empire. Forrest flatly refused, so Archer forged orders from Starfleet Command; which approved the situation and authorized him to lead a mutiny on Forrest and steal the Defiant. The mutiny worked perfectly and Forrest was imprisoned. Archer proceeded to make T'Pol his first officer and then assigned her and his chief engineer, Commander Charles Tucker III, to install an ill-gotten Sulibancloaking device to prevent their discovery. Archer then captured the Tholian pilot, and after much brutal interrogation, gained the location of the ship: in the Vintaak system. Archer secretly encrypted the navigator's controls to prevent anyone altering course, which later proved useful. After T'Pol aided Forrest in regaining his command, Forrest couldn't kill Archer as he alone knew the code to unlock the controls. So instead, the Adm. threw his "ex"-exec in Malcolm Reed's newly-made agony booth for a record 10 hours. Forrest, at Starfleet's behest, was forced to continue the mission. When the Enterprise arrived, Archer led an away team to capture the Defiant (unaware of Forrest's secret order to T'Pol to kill Archer), however Enterprise was discovered and destroyed by Tholian warships. Archer and the team were successful in partially restoring weapons, shields and impulse engines, destroying most of the warships and the drydock itself. Archer then rescued the 47 Enterprise survivors (excluding Forrest; who died on his ship) and sped towards Terran space. (ENTepisode: "In a Mirror, Darkly")

Archer and the crew set about restoring the partially-stripped ship, and put down Slar; a rogue Gorn worker that had attempted and failed to keep them at impulse speed. With the warp drive restored, Archer took the ship to rendezvous with the Terran assault fleet. While en-route, Archer looked up the file on his counterpart. He was disgusted at the mention of no Empire, but a "United Federation of Fools". Archer became insanely jealous when he learned his counterpart had a long, distinguished and respected career as a starship captain, diplomat and statesman (even having two planets named after him) and being noted by historian John Gill as "the greatest explorer in the 22nd century". This continuing obsession led Archer's mental health to deteriorate and made him suffer hallucinations of his prime-universe counterpart. When the Defiant eventually made it to the rendezvous point, they found that the ISS Avenger, under the command of AdmiralGregory Black, was the only surviving Starfleet vessel and was quickly being damaged by four rebel ships. Archer promptly destroyed the rebels (except for one critically-damaged Andoriancruiser which Archer let go to spread word to the Rebellion) and welcomed Black on board the Defiant to update him on current developments. Black was grateful to Archer for both his intervention in the battle and for obtaining the Defiant, and assured Archer he would be promoted at the earliest opportunity. When Archer asked for an immediate, field commission and command of Defiant on a permanent basis, Black refused, stating he wanted to take the ship back to Earth as a trophy and have it reverse-engineered and learn about its technology. Archer, fed up with the continuing losses suffered by the Empire, its corrupt leadership, the setbacks his own career was suffering, and the realization that Black would most likely take all the credit for his achievements caused him to finally reach his breaking point. Archer, declaring himself a captain, took out a salvaged 23rd centuryphaser and disintegrated Black, claiming the Defiant for himself. (ENTepisode: "In a Mirror, Darkly")

Archer unveiled his most ambitious plan yet to the assembled Defiant and Avenger crews: to take the Defiant back to Earth and seize control of the Empire itself, with Archer as Emperor and then put down the Rebellion. He argued that the problem with the Empire was its leadership, something many others among the crew believed in, and quickly gained the support of his new crewmembers. Archer grew more and more anti-alien in his views while on course for Earth, as he believed they were holding Humanity back (much like his counterpart, but for different reasons). In his new paranoia, he ordered all alien crewmembers on the Defiant transferred to the Avenger (with the exception of Phlox, whom he believed to not be a threat-as his people are pacifists) and the humans from Avenger to be brought on the Defiant. Archer later destroyed the Avenger when its alien crew rebelled. Just as the Defiant arrived, Archer died from the effects of poisoning by Sato (with help from his trusted bodyguardSergeantTravis Mayweather) as she sought to take the Terran Empire crown for herself. The reign of "Emperor Jonathan Archer" was over before it began. (ENTepisode: "In a Mirror, Darkly")

He was further conditioned by Regent T'Pol to be fiercely loyal to Empress Sato the First, and obey her every order. However, while Phlox's work held, T'Pol's did not and Archer defected to the Rebellion after two years of service. He rose to prominence quickly, debunking the Imperial myth that the Defiant came from a future Terran Empire and fostering support for a new government modeled after the parallel universe Federation. As a symbol of this support, the rebels adopted the uniforms of the 23rd centuryStarfleet. In 2165, a new threat to the Rebellion would present itself in the Nobunaga, a copy of the Defiant built by order of the Empress herself, with construction overseen by CommanderCharles Tucker III.

In desperation, Archer contacted Tucker, pleading for his help in destroying the new starship, voicing their mutual fear of what Sato could accomplish with both ships under her command. Motivated by that fear, Tucker instead provided Archer with the prefix codes for the Nobunaga, allowing the Rebellion to seize the ship and turn it against the Empire. (ENT - Mirror Universeshort story: "Nobunaga")